It is believed that the San José Brush Rabbit is closely related to the Brush Rabbit (S. bachmani) from mainland Baja California (Chapman 1974, Thomas and Best 1994, Cervantes et al. 1999). The San José Brush Rabbit may be distinguished from the Brush Rabbit by its larger ears and paler pelage (Nelson 1907). Genetic and taxonomic studies are necessary to clarify the relationship between these two species (Chapman et al. 1990). No subspecies are recognized.

Justification:
The San José Brush Rabbit is an endemic rabbit species on San José Island. It is represented by one population restricted to a specific habitat characterized by a high richness of brush and trees species. The extent of occurrence and area of occupancy within this one population are currently the same: 20 km². Informal surveys conducted in 1995 and 1996 were compared with quantitative surveys in 2008 and it was assessed that the population of the rabbits had declined, although these differences were not quantified. There are known demonstrable threats to the species: predation by feral cats (and maybe dogs), habitat loss due to competition with feral goats, illegal hunting by local people, and the potential development of a resort and activation of a salt mine in or near prime habitat occupied by the rabbit.

The San José Brush Rabbit is found only on San José Island (approximate total area is 170 km²) in the Gulf of California, Baja California Sur, Mexico, just north of the city of La Paz. Due to a lack of field investigations, prior assessments assumed that the San José Brush Rabbit occupied the entire island (Romero and Rangel 2008). Recent detailed, island-wide surveys (1995, 1996, 2008) have determined that the rabbit occupies only a restricted range of approximately 20 km² along the southwest coastal plain (Lorenzo et al. 2011). This area constitutes a single continuous population, thus the extent of occurrence (EOO) is equivalent to the area of occupancy (AOO).

Fewer San José Brush Rabbits were observed in the area of occupancy (AOO) in 2008 compared with observations in 1995 and 1996, although these differences were not quantified. In 2008 the population density of the San José Brush Rabbit was estimated to be 25–35 individuals/km² in an area of optimal habitat of approximately 4 km² within the AOO. This species is abundant in areas characterized by a high richness of brush and trees species (Lorenzo et al. 2011).

The San José Brush Rabbit was found reproductively active in November. The rabbit is most active between sunset and 02:00 hr and from about 06:00–10:00 hr (Lorenzo et al. 2011).

The San José Brush Rabbit shares its habitat with one of the most diverse mammal faunas on the islands in the Gulf of California, including the Critically Endangered San Jose Island Kangaroo Rat (Dipodomys insularis) (Thomas and Best 1994, Lorenzo et al. 2011).

All wildlife on San José Island is protected under Mexican law (SEMARNAT 2002), but local people or fishers often illegally kill protected Mule Deer (Odocoileus hemionus) and San José Brush Rabbits when they are legally hunting invasive goats (Lorenzo et al. 2011). This activity can be a threat to the global rabbit population, although more information is necessary to document the extent of the hunting. Also, feral goats may negatively compete with the rabbits by eating and destroying native vegetation (Gómez 2006).

Predation by native and non-native species constitutes a threat to the global population of the San José Brush Rabbit. The most serious threat is by feral cats which frequent the area of occupancy and commonly prey on rabbits (Espinosa-Gayosso and Álvarez-Castañeda 2006, Lorenzo et al. 2011). Domestic dogs in areas occupied by people may also constitute a predation threat to the rabbits. Predation by cats and maybe dogs is especially critical given the putative tameness of this insular species. It has also been felt that the Ringtail (Bassariscus astutus) may prey on rabbits, but Ringtails mainly live in the rocky hills and not in the area of rabbit occupancy on the island, thus they may be only occasional and opportunistic predators (Lorenzo et al. 2011). Several other species on San José Island could prey on rabbits: Rattlesnakes (Crotalus enyo enyo, C. mitchelli mitchelli, C. ruber lucanensis); Gopher Snakes (Pituophis melanoleucus bimaris, P. vertebralis); Osprey (Pandion haliaetus); Red-tailed Hawk (Buteo jamaicensis); Peregrine falcon (Falco peregrinus); and American Kestrel (F. sparverius) (Cody and Velarde 2002, Espinosa-Gayosso and Álvarez-Castañeda 2006).

The most important threat to the San José Brush Rabbit is related to human development activities, in spite of their protected status on San José Island under Mexican law (SEMARNAT 2002). Plans for a resort are being developed with an accompanying golf course, private airport and small marina in prime habitat occupied by the rabbit. This development would cause a loss of habitat (area of occupancy) of the rabbit, including breeding and reproduction sites. Additionally, a salt mine close to the area of highest rabbit density may be activated in the near future, and this facility could be used for worker housing and equipment storage. Free-ranging dogs and cats of the workers would then contribute to further predation on the rabbit (Lorenzo et al. 2011).

The San José Brush Rabbit is fully protected on San José Island, along with all native wildlife (SEMARNAT 2002), but there is little enforcement of this protected status. Enforcement of the protected status of rabbits should be enhanced, with a goal to stop all collateral hunting of rabbits on the island.

Given that feral cats constitute a major threat to the San José Brush Rabbit (as well as other Critically Endangered species, such as the San José Island Kangaroo Rat), their extirpation is a high priority. Also, to reduce habitat loss and competition due to feral goats, the goats should similarly be eradicated from the island.

Before any development of the resort or activation of the salt mine occurs, a full environmental impact study should be conducted that addresses specifically how these developments might impact Critically Endangered mammals on the island and outlines potential mitigation should the projects be approved.

Given the tenuous foothold that the San José Brush Rabbit has on San José Island, future studies on their genetics and potential for inbreeding depression should be conducted.

A long-term monitoring system should be enacted so that the trend analysis of the San José Brush Rabbit population can be used to determine how best, going forward, this species should be managed.